Around 1985, Jones became interested in anomalous concentrations of helium-3 and Tritium found in gases escaping from volcanoes. He hypothesized that metals and high pressures in the Earth's interior might make fusion more likely, and began a series of experiments on what he referred to as geo-fusion, or piezofusion, high-pressure fusion. To characterize the reactions, Jones designed and constructed a neutron counter that was capable of accurately measuring minuscule numbers of neutrons produced in his experiments. The counter indicated that a small amount of fusion was occurring. Jones claimed that the results indicate that fusion is at least possible, although the process was unlikely to be useful as an energy source.

In the mid-1980s, Jones and other BYU scientists worked on what he referred to as Cold Nuclear Fusion in a Scientific American article (the process is currently known as muon-catalyzed fusion to avoid confusion with the cold fusion concept proposed by Pons and Fleischman). Muon-catalyzed fusion was a field of some interest during the 1980s as a potential energy source; however, its low energy output appears to be unavoidable (because of alpha-muon sticking losses). Jones led a research team that, in 1986, achieved 150 fusions per muon (average), releasing over 2,600 MeV of fusion energy per muon, a record which still stands.[17]

Stanley Pons and Martin Fleischmann commenced their work at approximately the same time. Jones became aware of their work when they applied for research funding from the DOE, after which the DOE forwarded their proposal to Jones for peer review. When Jones realized that their work was similar, he and Pons and Fleischmann agreed to release their papers to Nature on the same day (March 24, 1989). However, Pons and Fleischmann announced their results at a press event the day before. Jones faxed his paper to Nature.[18]

A New York Times article says that although peer reviewers were harshly critical of Pons' and Fleischmann's research, they did not apply such criticism to Jones' significantly more modest, theoretically supported findings. Although critics insisted that Jones' results were probably caused by experimental error,[19] the majority of the reviewing physicists claimed that he was a careful scientist. Later research and experiments have supported Jones' metallic "cold fusion" (geo-fusion) reports.[20]

On September 22, 2005 Jones presented his views on the collapse of the World Trade Center towers and World Trade Center 7 at a BYU seminar attended by approximately 60 people. Jones claimed that a variety of evidence defies the mainstream collapse theory and favors controlled demolition, using thermite. The evidence Jones cited included the speed and symmetry of the collapses, and characteristics of dust jets. Later, Jones claimed he had identified grey/red flakes found in the dust as nanothermite traces. He has also claimed that the thermite reaction products (aluminium oxide and iron-rich microspheres) were also found in the dust.[22] He called for further scientific investigation to test the controlled demolition theory and the release of all relevant data by the government.[23] Shortly after the seminar, Jones placed a research paper entitled "Why Indeed Did the WTC Buildings Collapse?" on his page in the Physics department Web site, noting that BYU had no responsibility for the paper.[24]

Jones subsequently presented the WTC research in lectures at Idaho State University, Utah Valley State College, University of Colorado at Boulder and University of Denver, the Utah Academy of Science, Sonoma State University, University of California at Berkeley, and the University of Texas at Austin.[25][26][27][28][29][30][31]

On September 7, 2006, Jones removed his paper from BYU's website at the request of administrators and was placed on paid leave.[32] The university cited its concern about the "increasingly speculative and accusatory nature" of Jones' work and that perhaps Jones' research had "not been published in appropriate scientific venues" as reasons for putting him under review. The review was to have been conducted at three levels: BYU administration, the College of Physical and Mathematical Sciences, and the Physics Department.[33] However, BYU discontinued the review.[8] Some of Jones' colleagues also defended Jones' 9/11 work to varying degrees,[34] and Project Censored lists his 9/11 research among the top mainstream media censored stories of 2007.[35]

Jones has been interviewed by mainstream news sources and has made a number of public appearances. Although Jones has urged caution in drawing conclusions,[37] some believe that his public comments have indicated a significant degree of certainty on the controlled demolition of the World Trade Center and the culpability of elements within the U.S. government.[38] In one interview, Jones directly called into question the government's theory regarding the attacks and subsequent uncharacteristic total destruction of the buildings, stating that "we don't believe that 19 hijackers and a few others in a cave in Afghanistan pulled this off acting alone".[39] His name is often mentioned in reporting about 9/11 conspiracy theories.[40]

Jones has published several papers suggesting that the World Trade Center was demolished with explosives, but his 2005 paper, "Why Indeed Did the WTC Buildings Collapse?" was his first paper on the topic and was considered controversial both for its content and its claims to scientific rigor.[41] Jones' early critics included members of BYU's engineering faculty;[42] shortly after he made his views public, the BYU College of Physical and Mathematical Sciences and the faculty of structural engineering issued statements in which they distanced themselves from Jones' work. They noted that Jones' "hypotheses and interpretations of evidence were being questioned by scholars and practitioners," and expressed doubts on whether they had been "submitted to relevant scientific venues that would ensure rigorous technical peer review."[43] Jones further presented and defended his research before peers at the Utah Academy of Sciences, Arts and Letters on 7 April 2006 at nearby Snow College.[44] Jones maintained that the paper was peer-reviewed prior to publication within a book "9/11 and American Empire: Intellectuals Speak Out" by D.R. Griffin.[45] The paper was published in the online "Journal of 9/11 Studies", a journal co-founded and co-edited by Jones for the purpose of "covering the whole of research related to 9/11/2001." The paper also appeared in a volume of essays edited by David Ray Griffin and Peter Dale Scott.[46]

In April 2008, Jones, along with four other authors, published a letter in The Bentham Open Civil Engineering Journal, titled, 'Fourteen Points of Agreement with Official Government Reports on the World Trade Center Destruction'.[47] In August 2008, Jones, along with Kevin Ryan and James Gourley, published a peer-reviewed article in The Environmentalist, titled, 'Environmental anomalies at the World Trade Center: Evidence for energetic materials'.[48]

In April 2009, Jones, along with Niels H. Harrit and 7 other authors published a paper in The Open Chemical Physics Journal, titled, 'Active Thermitic Material Discovered in Dust from the 9/11 World Trade Center Catastrophe'.[49] The editor of the journal, Professor Marie-Paule Pileni, an expert in explosives and nano-technology,[50][51] resigned. She received an e-mail from the Danish science journal Videnskab asking for her professional assessment of the article's content.[52][53] According to Pileni, the article was published without her authorization. Subsequently, numerous concerns arose regarding the reliability of the publisher, Bentham Science Publishing. This included the publishing an allegedly peer reviewed article generated by SCIgen[54] (although this program has also successfully submitted papers to IEEE and Springer[55]), the resignation of multiple people at the administrative level,[56][57] and soliciting article submissions from researchers in unrelated fields through spam.[58] With regard to the peer review process of the research conducted by Jones in The Open Chemical Physics Journal, Dr. David Griscom identified himself as one of the reviewers.[59] The paper which Jones co-authored referenced Dr. Griscom, and multiple scientists studying 9/11, in the acknowledgements for "elucidating discussions and encouragements".[22] Almost four years prior to identifying himself as a reviewer and the welcome he received from Jones for speaking out boldly,[60] Griscom published a letter in defense of evidence-based 9/11 studies;[61] of which Jones was an editor.[62]

Europhysics News in August 2016 published "15 Years Later: On the Physics of High-rise Building Collapses," which strongly challenges the official U.S. Government (NIST) narrative of the collapse of WTC7 and the WTC Towers.[9] The paper was authored by Steven Jones, Robert Korol, Anthony Szamboti and Ted Walter.

Jones was a founding member of Scholars for 9/11 Truth for approximately one year as co-chair with James H. Fetzer. From mid-November 2006 until the end of that year, Jones, Fetzer and a series of other researchers and individuals engaged in a dispute about the direction of the organization. Jones and others examined the claims of James Fetzer and Judy Wood — i.e., that directed energy weapons or mini-nukes destroyed the WTC Towers — and delineated empirical reasons for rejecting them.[63]

In December 2006, Steven Jones and about 4/5ths of the members voted to leave the Scholars for 9/11 Truth organization[64] to establish Scholars for 9/11 Truth & Justice.[65] While Jones is not a committee member of Scholars for 9/11 Truth & Justice, his work is supported and documented by the group. By April 2010, that organization had grown to over 800 members.[66]

^Jones, Steven E. "Why Indeed Did the WTC Buildings Collapse?". Retrieved September 9, 2008. I presented my objections to the “official” theory at a seminar at BYU on September 22, 2005, to about 60 people. I also showed evidence and scientific arguments for the explosive demolition theory.

^ abGravois, John (June 23, 2006). "Professors of Paranoia?". The Chronicle of Higher Education. 52 (42). p. A.10. Retrieved September 14, 2016. Soon after Mr. Jones posted his paper online, the physics department at Brigham Young moved to distance itself from his work. The department released a statement saying that it was 'not convinced that his analyses and hypotheses have been submitted to relevant scientific venues that would ensure rigorous technical peer review.'

^McIlvain, Ryan (December 5, 2005). "Censor rumors quelled". BYU NewsNet. Retrieved September 4, 2007. Professor Jones’s department and college administrators are not convinced that his analyses and hypotheses have been submitted to relevant scientific venues that would ensure rigorous technical peer review. The structural engineering faculty in the Fulton College of Engineering and Technology do not support the hypotheses of Professor Jones.